1
|
Chen G, Zhang Z. IDRWalker: A Random Walk Based Tool for Generating Intrinsically Disordered Regions in Large Protein Complexes. ACS OMEGA 2024; 9:32059-32065. [PMID: 39072126 PMCID: PMC11270708 DOI: 10.1021/acsomega.4c04161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/16/2024] [Accepted: 06/27/2024] [Indexed: 07/30/2024]
Abstract
Intrinsically disordered regions (IDRs), which may be functionally important, are common in proteins. However, the structures of IDRs are often missing due to their highly dynamic nature. In the study of IDRs, integrative modeling combining computational simulations and experimental data is a common approach, for which initial structures of the IDRs need to be built. However, applying this method to large protein complexes is challenging because existing structure generation tools are sometimes unsuitable for IDRs in large systems. To facilitate convenient and rapid structure generation of IDRs in large protein complexes, we developed a computational tool named IDRWalker based on self-avoiding random walks. Three protein complexes were used to illustrate the efficiency of the tool, and it was found that IDRs in more than 800 chains of the nuclear pore complex could be generated in minutes. These structures of large protein complexes with added IDRs can be further used to run computational simulations for integrative modeling.
Collapse
Affiliation(s)
- Guanglin Chen
- Department
of Physics, University of Science and Technology
of China, Hefei, Anhui 230026, PR China
| | - Zhiyong Zhang
- Department
of Physics, University of Science and Technology
of China, Hefei, Anhui 230026, PR China
- MOE
Key Laboratory for Cellular Dynamics, University of Science and Technology
of China, Hefei, Anhui 230026, PR
China
| |
Collapse
|
2
|
Young BD, Cook ME, Costabile BK, Samanta R, Zhuang X, Sevdalis SE, Varney KM, Mancia F, Matysiak S, Lattman E, Weber DJ. Binding and Functional Folding (BFF): A Physiological Framework for Studying Biomolecular Interactions and Allostery. J Mol Biol 2022; 434:167872. [PMID: 36354074 PMCID: PMC10871162 DOI: 10.1016/j.jmb.2022.167872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 09/20/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022]
Abstract
EF-hand Ca2+-binding proteins (CBPs), such as S100 proteins (S100s) and calmodulin (CaM), are signaling proteins that undergo conformational changes upon increasing intracellular Ca2+. Upon binding Ca2+, S100 proteins and CaM interact with protein targets and induce important biological responses. The Ca2+-binding affinity of CaM and most S100s in the absence of target is weak (CaKD > 1 μM). However, upon effector protein binding, the Ca2+ affinity of these proteins increases via heterotropic allostery (CaKD < 1 μM). Because of the high number and micromolar concentrations of EF-hand CBPs in a cell, at any given time, allostery is required physiologically, allowing for (i) proper Ca2+ homeostasis and (ii) strict maintenance of Ca2+-signaling within a narrow dynamic range of free Ca2+ ion concentrations, [Ca2+]free. In this review, mechanisms of allostery are coalesced into an empirical "binding and functional folding (BFF)" physiological framework. At the molecular level, folding (F), binding and folding (BF), and BFF events include all atoms in the biomolecular complex under study. The BFF framework is introduced with two straightforward BFF types for proteins (type 1, concerted; type 2, stepwise) and considers how homologous and nonhomologous amino acid residues of CBPs and their effector protein(s) evolved to provide allosteric tightening of Ca2+ and simultaneously determine how specific and relatively promiscuous CBP-target complexes form as both are needed for proper cellular function.
Collapse
Affiliation(s)
- Brianna D Young
- The Center for Biomolecular Therapeutics (CBT), Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Mary E Cook
- The Center for Biomolecular Therapeutics (CBT), Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Brianna K Costabile
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Riya Samanta
- Biophysics Graduate Program, University of Maryland, College Park, MD 20742, USA; Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
| | - Xinhao Zhuang
- The Center for Biomolecular Therapeutics (CBT), Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Spiridon E Sevdalis
- The Center for Biomolecular Therapeutics (CBT), Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Kristen M Varney
- The Center for Biomolecular Therapeutics (CBT), Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Silvina Matysiak
- Biophysics Graduate Program, University of Maryland, College Park, MD 20742, USA; Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
| | - Eaton Lattman
- The Center for Biomolecular Therapeutics (CBT), Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - David J Weber
- The Center for Biomolecular Therapeutics (CBT), Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA; The Institute of Bioscience and Biotechnology Research (IBBR), Rockville, MD 20850, USA.
| |
Collapse
|
3
|
Kobayashi T, Tsutsumi A, Kurebayashi N, Saito K, Kodama M, Sakurai T, Kikkawa M, Murayama T, Ogawa H. Molecular basis for gating of cardiac ryanodine receptor explains the mechanisms for gain- and loss-of function mutations. Nat Commun 2022; 13:2821. [PMID: 35595836 PMCID: PMC9123176 DOI: 10.1038/s41467-022-30429-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 04/28/2022] [Indexed: 12/12/2022] Open
Abstract
Cardiac ryanodine receptor (RyR2) is a large Ca2+ release channel in the sarcoplasmic reticulum and indispensable for excitation-contraction coupling in the heart. RyR2 is activated by Ca2+ and RyR2 mutations are implicated in severe arrhythmogenic diseases. Yet, the structural basis underlying channel opening and how mutations affect the channel remains unknown. Here, we address the gating mechanism of RyR2 by combining high-resolution structures determined by cryo-electron microscopy with quantitative functional analysis of channels carrying various mutations in specific residues. We demonstrated two fundamental mechanisms for channel gating: interactions close to the channel pore stabilize the channel to prevent hyperactivity and a series of interactions in the surrounding regions is necessary for channel opening upon Ca2+ binding. Mutations at the residues involved in the former and the latter mechanisms cause gain-of-function and loss-of-function, respectively. Our results reveal gating mechanisms of the RyR2 channel and alterations by pathogenic mutations at the atomic level. Ryanodine receptor 2 (RyR2) is a Ca2+ release channel essential for cardiac excitation-contraction coupling. Here, the authors use structural and functional analysis to reveal RyR2 gating mechanism and its alterations by pathogenic mutations.
Collapse
Affiliation(s)
- Takuya Kobayashi
- Department of Cellular and Molecular Pharmacology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Akihisa Tsutsumi
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Nagomi Kurebayashi
- Department of Cellular and Molecular Pharmacology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Kei Saito
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Masami Kodama
- Department of Cellular and Molecular Pharmacology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Takashi Sakurai
- Department of Cellular and Molecular Pharmacology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Masahide Kikkawa
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takashi Murayama
- Department of Cellular and Molecular Pharmacology, Juntendo University Graduate School of Medicine, Tokyo, Japan.
| | - Haruo Ogawa
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan.
| |
Collapse
|
4
|
Wang QL, Fang Y, Jin SG, Liang JT, Ren YF. Atypical symptoms of malignant hyperthermia: A rare causative mutation in the RYR1 gene. Open Med (Wars) 2022; 17:239-244. [PMID: 35178478 PMCID: PMC8812711 DOI: 10.1515/med-2021-0396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 11/15/2022] Open
Abstract
Malignant hyperthermia (MH) is an autosomal dominant genetic condition of the skeletal muscle triggered by inhaled general anesthetic agents or succinylcholine and associated with a hypermetabolic state and skeletal muscle rigidity. Tachycardia, increased carbon dioxide production, hypercarbia, hyperthermia, acidosis, hyperkalemia, cardiac arrhythmias, muscle rigidity, and rhabdomyolysis are common symptoms of MH. As the progression of the syndrome could be rapid or less evident, even experienced physicians have difficulty in diagnosing MH, which can lead to delays in treatment and increased mortality. We report a rare case of a 36-year-old man, who underwent open reduction and internal fixation of the left clavicle after inhaled anesthetics. The patient developed dyspnea, hypotension, unremitting hyperthermia, tachycardia, and elevated serum myoglobin, and finally died of pyemia and disseminated intravascular coagulation. We reviewed the process of disease development, summarized the steps of diagnosis, and improved genetic testing. Exome sequencing revealed a new mutation c.8519G>A (p.arg2840 GLN) in the RYR1 gene that could be associated with MH. The gene mutation was also found in his daughter’s genetic test. This case emphasized the importance of the awareness of MH and its atypical clinical symptoms. The presence of dyspnea, hypotension, unremitting hyperthermia, tachycardia, and raised myoglobin in serum might further strengthen the clinical diagnosis of suspected MH.
Collapse
Affiliation(s)
- Qiao Ling Wang
- Department of Ministry of Science, Hospital of Chengdu University of Traditional Chinese Medicine , Chengdu , Sichuan, 610072 , China
| | - Yu Fang
- Department of Ministry of Science, Hospital of Chengdu University of Traditional Chinese Medicine , Chengdu , Sichuan, 610072 , China
| | - Shuo Guo Jin
- Department of Ministry of Science, Hospital of Chengdu University of Traditional Chinese Medicine , Chengdu , Sichuan, 610072 , China
| | - Jing Tao Liang
- Department of Ministry of Science, Hospital of Chengdu University of Traditional Chinese Medicine , Chengdu , Sichuan, 610072 , China
| | - Yi Feng Ren
- Department of Ministry of Science, Hospital of Chengdu University of Traditional Chinese Medicine , Chengdu , Sichuan, 610072 , China
| |
Collapse
|
5
|
Huang T, Jian X, Liu J, Zheng L, Li FQ, Meng D, Wang T, Zhang S, Liu Y, Guan Z, Feng J. Exercise and/or Cold Exposure Alters the Gene Expression Profile in the Fat Body and Changes the Heart Function in Drosophila. Front Endocrinol (Lausanne) 2022; 13:790414. [PMID: 35418948 PMCID: PMC8995477 DOI: 10.3389/fendo.2022.790414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 02/25/2022] [Indexed: 12/18/2022] Open
Abstract
The major reason of human morbidity and mortality is obesity and related diseases. Brown adipose tissue (BAT) is associated with low total adipose tissue content and a lower risk of type 2 diabetes mellitus. Studies have shown that exercise and cold expose may induce browning. In this study, we verified (1) whether exercise and/or cold exposure can improve the expression level of ucp4c, serca, ampkα, camkII, sirt1, octβ3r, and hamlet; (2) if these interventions can save cardiac dysfunction induced by a high-fat diet (HFD) in Drosophila. w1118 (wild-type) virgin female flies collected within 8 h after eclosion were divided into eight groups: the normal feed control group (NFD-C), the normal feed exercise group (NFD-E), the normal feed cold exposure group (NFD-CA), the normal feed exercise/cold exposure group (NFD-EC), the HFD control group (HFD-C), the HFD exercise group (HFD-E), the HFD cold exposure group (HFD-CA), and the HFD exercise/cold exposure group (HFD-EC). After exercise and/or cold exposure for 7 days, the mRNA expression levels of ucp4c, serca, ampkα, camk II, sirt1, octβ3r, and hamlet were tested by qRT-PCR, and m-mode was used to assess cardiac function. In addition, we assessed the triacylglycerol (TAG) levels, motor ability, fat mass (by Oil Red O [ORO] staining), and morphological features. The results of TAG, ORO staining, and morphological features all indicate that after interventions, body size of Drosophila was smaller compared with the control group, irrespective of the feeding patterns. The mRNA expression levels of ucp4c, serca, octβ3r, hamlet, ampkα, camkII, and sirt1 were changed to varying degrees under different intervention states (exercise and/or cold exposure). Cold exposure and exercise/cold exposure partly improved cardiac function and the normal fruit flies' cardiac function and exercise ability. However, after exercise intervention, exercise ability and heart function were improved in both HFD and normal-fat diet (NFD) fruit flies. In conclusion, different intervention states (exercise and/or cold exposure) can change the mRNA expression levels of ucp4c, serca, octβ3r, hamlet, ampkα, camkII, and sirt1. Exercise is the most effective way to restore HFD-induced cardiac dysfunction.
Collapse
|
6
|
Yuan Q, Dridi H, Clarke OB, Reiken S, Melville Z, Wronska A, Kushnir A, Zalk R, Sittenfeld L, Marks AR. RyR1-related myopathy mutations in ATP and calcium binding sites impair channel regulation. Acta Neuropathol Commun 2021; 9:186. [PMID: 34809703 PMCID: PMC8609856 DOI: 10.1186/s40478-021-01287-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 10/31/2021] [Indexed: 11/10/2022] Open
Abstract
The type 1 ryanodine receptor (RyR1) is an intracellular calcium (Ca2+) release channel on the sarcoplasmic/endoplasmic reticulum that is required for skeletal muscle contraction. RyR1 channel activity is modulated by ligands, including the activators Ca2+ and ATP. Patients with inherited mutations in RyR1 may exhibit muscle weakness as part of a heterogeneous, complex disorder known as RYR1-related myopathy (RYR1-RM) or more recently termed RYR1-related disorders (RYR1-RD). Guided by high-resolution structures of skeletal muscle RyR1, obtained using cryogenic electron microscopy, we introduced mutations into putative Ca2+ and ATP binding sites and studied the function of the resulting mutant channels. These mutations confirmed the functional significance of the Ca2+ and ATP binding sites identified by structural studies based on the effects on channel regulation. Under normal conditions, Ca2+ activates RyR1 at low concentrations (µM) and inhibits it at high concentrations (mM). Mutations in the Ca2+-binding site impaired both activating and inhibitory regulation of the channel, suggesting a single site for both high and low affinity Ca2+-dependent regulation of RyR1 function. Mutation of residues that interact with the adenine ring of ATP abrogated ATP binding to the channel, whereas mutating residues that interact with the triphosphate tail only affected the degree of activation. In addition, patients with mutations at the Ca2+ or ATP binding sites suffer from muscle weakness, therefore impaired RyR1 channel regulation by either Ca2+ or ATP may contribute to the pathophysiology of RYR1-RM in some patients.
Collapse
|
7
|
Baker ML, Dirksen RT, Hamilton SL. How mutations in RYR1 that cause malignant hyperthermia increase RYR1 sensitivity to activators. Cell Calcium 2021; 97:102412. [PMID: 33905995 DOI: 10.1016/j.ceca.2021.102412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 11/30/2022]
Abstract
New electron cryomicroscopy structures of RYR1 show that mutations associated with Malignant Hyperthermia drive conformational changes in the cytoplasmic domains of the closed channel to more closely resemble those of the open channel.
Collapse
Affiliation(s)
- Matthew L Baker
- Department of Biochemistry and Molecular Biology, University of Texas Health Science Center, Houston, TX, 77030, United States
| | - Robert T Dirksen
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY, 14642, United States
| | - Susan L Hamilton
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, United States.
| |
Collapse
|
8
|
Gong D, Yan N, Ledford HA. Structural Basis for the Modulation of Ryanodine Receptors. Trends Biochem Sci 2020; 46:489-501. [PMID: 33353849 DOI: 10.1016/j.tibs.2020.11.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 11/16/2020] [Accepted: 11/20/2020] [Indexed: 12/11/2022]
Abstract
Historically, ryanodine receptors (RyRs) have presented unique challenges for high-resolution structural determination despite long-standing interest in their role in excitation-contraction coupling. Owing to their large size (nearly 2.2 MDa), high-resolution structures remained elusive until the advent of cryogenic electron microscopy (cryo-EM) techniques. In recent years, structures for both RyR1 and RyR2 have been solved at near-atomic resolution. Furthermore, recent reports have delved into their more complex structural associations with key modulators - proteins such as the dihydropyridine receptor (DHPR), FKBP12/12.6, and calmodulin (CaM), as well as ions and small molecules including Ca2+, ATP, caffeine, and PCB95. This review addresses the modulation of RyR1 and RyR2, in addition to the impact of such discoveries on intracellular Ca2+ dynamics and biophysical properties.
Collapse
Affiliation(s)
- Deshun Gong
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province/Key Laboratory of Growth Regulation and Transformation Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang Province, China.
| | - Nieng Yan
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
| | - Hannah A Ledford
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
| |
Collapse
|
9
|
Ogawa H, Kurebayashi N, Yamazawa T, Murayama T. Regulatory mechanisms of ryanodine receptor/Ca 2+ release channel revealed by recent advancements in structural studies. J Muscle Res Cell Motil 2020; 42:291-304. [PMID: 32040690 PMCID: PMC8332584 DOI: 10.1007/s10974-020-09575-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 02/05/2020] [Indexed: 02/07/2023]
Abstract
Ryanodine receptors (RyRs) are huge homotetrameric Ca2+ release channels localized to the sarcoplasmic reticulum. RyRs are responsible for the release of Ca2+ from the SR during excitation–contraction coupling in striated muscle cells. Recent revolutionary advancements in cryo-electron microscopy have provided a number of near-atomic structures of RyRs, which have enabled us to better understand the architecture of RyRs. Thus, we are now in a new era understanding the gating, regulatory and disease-causing mechanisms of RyRs. Here we review recent advances in the elucidation of the structures of RyRs, especially RyR1 in skeletal muscle, and their mechanisms of regulation by small molecules, associated proteins and disease-causing mutations.
Collapse
Affiliation(s)
- Haruo Ogawa
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan.
| | - Nagomi Kurebayashi
- Department of Pharmacology, Juntendo University School of Medicine, Tokyo, 113-8421, Japan
| | - Toshiko Yamazawa
- Department of Molecular Physiology, The Jikei University School of Medicine, Tokyo, 105-8461, Japan
| | - Takashi Murayama
- Department of Pharmacology, Juntendo University School of Medicine, Tokyo, 113-8421, Japan
| |
Collapse
|
10
|
King MM, Kayastha BB, Franklin MJ, Patrauchan MA. Calcium Regulation of Bacterial Virulence. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1131:827-855. [PMID: 31646536 DOI: 10.1007/978-3-030-12457-1_33] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Calcium (Ca2+) is a universal signaling ion, whose major informational role shaped the evolution of signaling pathways, enabling cellular communications and responsiveness to both the intracellular and extracellular environments. Elaborate Ca2+ regulatory networks have been well characterized in eukaryotic cells, where Ca2+ regulates a number of essential cellular processes, ranging from cell division, transport and motility, to apoptosis and pathogenesis. However, in bacteria, the knowledge on Ca2+ signaling is still fragmentary. This is complicated by the large variability of environments that bacteria inhabit with diverse levels of Ca2+. Yet another complication arises when bacterial pathogens invade a host and become exposed to different levels of Ca2+ that (1) are tightly regulated by the host, (2) control host defenses including immune responses to bacterial infections, and (3) become impaired during diseases. The invading pathogens evolved to recognize and respond to the host Ca2+, triggering the molecular mechanisms of adhesion, biofilm formation, host cellular damage, and host-defense resistance, processes enabling the development of persistent infections. In this review, we discuss: (1) Ca2+ as a determinant of a host environment for invading bacterial pathogens, (2) the role of Ca2+ in regulating main events of host colonization and bacterial virulence, and (3) the molecular mechanisms of Ca2+ signaling in bacterial pathogens.
Collapse
Affiliation(s)
- Michelle M King
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Biraj B Kayastha
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Michael J Franklin
- Department of Microbiology and Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA
| | - Marianna A Patrauchan
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA.
| |
Collapse
|
11
|
Hartel AJW, Shekar S, Ong P, Schroeder I, Thiel G, Shepard KL. High bandwidth approaches in nanopore and ion channel recordings - A tutorial review. Anal Chim Acta 2019; 1061:13-27. [PMID: 30926031 PMCID: PMC6860018 DOI: 10.1016/j.aca.2019.01.034] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 01/05/2019] [Indexed: 01/01/2023]
Abstract
Transport processes through ion-channel proteins, protein pores, or solid-state nanopores are traditionally recorded with commercial patch-clamp amplifiers. The bandwidth of these systems is typically limited to 10 kHz by signal-to-noise-ratio (SNR) considerations associated with these measurement platforms. At high bandwidth, the input-referred current noise in these systems dominates, determined by the input-referred voltage noise of the transimpedance amplifier applied across the capacitance at the input of the amplifier. This capacitance arises from several sources: the parasitic capacitance of the amplifier itself; the capacitance of the lipid bilayer harboring the ion channel protein (or the membrane used to form the solid-state nanopore); and the capacitance from the interconnections between the electronics and the membrane. Here, we review state-of-the-art applications of high-bandwidth conductance recordings of both ion channels and solid-state nanopores. These approaches involve tightly integrating measurement electronics fabricated in complementary metal-oxide semiconductors (CMOS) technology with lipid bilayer or solid-state membranes. SNR improvements associated with this tight integration push the limits of measurement bandwidths, in some cases in excess of 10 MHz. Recent case studies demonstrate the utility of these approaches for DNA sequencing and ion-channel recordings. In the latter case, studies with extended bandwidth have shown the potential for providing new insights into structure-function relations of these ion-channel proteins as the temporal resolutions of functional recordings matches time scales achievable with state-of-the-art molecular dynamics simulations.
Collapse
Affiliation(s)
- Andreas J W Hartel
- Bioelectronic Systems Laboratory, Department of Electrical Engineering, Columbia University, New York City, 10027, NY, USA.
| | - Siddharth Shekar
- Bioelectronic Systems Laboratory, Department of Electrical Engineering, Columbia University, New York City, 10027, NY, USA
| | - Peijie Ong
- Bioelectronic Systems Laboratory, Department of Electrical Engineering, Columbia University, New York City, 10027, NY, USA
| | - Indra Schroeder
- Plant Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany
| | - Gerhard Thiel
- Plant Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany
| | - Kenneth L Shepard
- Bioelectronic Systems Laboratory, Department of Electrical Engineering, Columbia University, New York City, 10027, NY, USA.
| |
Collapse
|
12
|
Joseph SK, Booth DM, Young MP, Hajnóczky G. Redox regulation of ER and mitochondrial Ca 2+ signaling in cell survival and death. Cell Calcium 2019; 79:89-97. [PMID: 30889512 DOI: 10.1016/j.ceca.2019.02.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 02/12/2019] [Accepted: 02/12/2019] [Indexed: 12/16/2022]
Abstract
Physiological signaling by reactive oxygen species (ROS) and their pathophysiological role in cell death are well recognized. This review focuses on two ROS targets that are key to local Ca2+ signaling at the ER/mitochondrial interface - notably, inositol trisphosphate receptors (IP3Rs) and the mitochondrial calcium uniporter (MCU). Both transport systems are central to molecular mechanisms in cell survival and death. Methods for the measurement of the redox state of these proteins and for the detection of ROS nanodomains are described. Recent results on the redox regulation of these proteins are reviewed.
Collapse
Affiliation(s)
- Suresh K Joseph
- MitoCare, Department of Pathology and Cell Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA.
| | - David M Booth
- MitoCare, Department of Pathology and Cell Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Michael P Young
- MitoCare, Department of Pathology and Cell Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - György Hajnóczky
- MitoCare, Department of Pathology and Cell Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| |
Collapse
|
13
|
Lindsay C, Sitsapesan M, Chan WM, Venturi E, Welch W, Musgaard M, Sitsapesan R. Promiscuous attraction of ligands within the ATP binding site of RyR2 promotes diverse gating behaviour. Sci Rep 2018; 8:15011. [PMID: 30301919 PMCID: PMC6177429 DOI: 10.1038/s41598-018-33328-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 09/26/2018] [Indexed: 12/31/2022] Open
Abstract
ATP is an essential constitutive regulator of cardiac ryanodine receptors (RyR2), enabling small changes in cytosolic Ca2+ to trigger large changes in channel activity. With recent landmark determinations of the full structures of RyR1 (skeletal isoform) and RyR2 using cryo-EM, and identification of the RyR1 ATP binding site, we have taken the opportunity to model the binding of fragments of ATP into RyR2 in order to investigate how the structure of the ATP site dictates the functional responses of ligands attracted there. RyR2 channel gating was assessed under voltage-clamp conditions and by [3H]ryanodine binding studies. We show that even the triphosphate (PPPi) moiety alone was capable of activating RyR2 but produced two distinct effects (activation or irreversible inactivation) that we suggest correspond to two preferred binding locations within the ATP site. Combinations of complementary fragments of ATP (Pi + ADP or PPi + AMP) could not reproduce the effects of ATP, however, the presence of adenosine prevented the inactivating PPPi effects, allowing activation similar to that of ATP. RyR2 appears to accommodate diverse types of molecules, including PPPi, deep within the ATP binding site. The most effective ligands, however, have at least three phosphate groups that are guided into place by a nucleoside.
Collapse
Affiliation(s)
- Chris Lindsay
- Department of Pharmacology, University of Oxford, Oxford, UK.,Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Mano Sitsapesan
- Department of Pharmacology, University of Oxford, Oxford, UK
| | - Wei Mun Chan
- Department of Pharmacology, University of Oxford, Oxford, UK
| | - Elisa Venturi
- Department of Pharmacology, University of Oxford, Oxford, UK
| | - William Welch
- University of Nevada School of Medicine, Department of Biochemistry, Reno, Nevada, USA
| | - Maria Musgaard
- Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, Oxford, UK. .,Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Canada.
| | | |
Collapse
|
14
|
Gaydukov AE, Balezina OP. Ryanodine- and CaMKII-dependent release of endogenous CGRP induces an increase in acetylcholine quantal size in neuromuscular junctions of mice. Brain Behav 2018; 8:e01058. [PMID: 29978952 PMCID: PMC6085904 DOI: 10.1002/brb3.1058] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 05/29/2018] [Accepted: 06/11/2018] [Indexed: 01/11/2023] Open
Abstract
OBJECTIVE The aim of this study was to identify the mechanism responsible for an increase in miniature endplate potentials (MEPPs) amplitude, induced by ryanodine as an agonist of ryanodine receptors in mouse motor nerve terminals. METHODS Using intracellular microelectrode recordings of MEPPs and evoked endplate potentials (EPPs), the changes in spontaneous and evoked acetylcholine release in motor synapses of mouse diaphragm neuromuscular preparations were studied. RESULTS Ryanodine (0.1 μM) increased both the amplitudes of MEPPs and EPPs to a similar extent (up to 130% compared to control). The ryanodine effect was prevented by blockage of receptors of calcitonin gene-related peptide (CGRP) by a truncated peptide CGRP8-37 . Endogenous CGRP is stored in large dense-core vesicles in motor nerve terminals and may be released as a co-transmitter. The ryanodine-induced increase in MEPPs amplitude may be fully prevented by inhibition of vesicular acetylcholine transporter by vesamicol or by blocking the activity of protein kinase A with H-89, suggesting that endogenous CGRP is released in response to the activation of ryanodine receptors. Activation of CGRP receptors can, in turn, upregulate the loading of acetylcholine into synaptic vesicles, which will increase the quantal size. This new feature of endogenous CGRP activity looks similar to recently described action of exogenous CGRP in motor synapses of mice. The ryanodine effect was prevented by inhibitors of Ca/Calmodulin-dependent kinase II (CaMKII) KN-62 or KN-93. Inhibition of CaMKII did not prevent the increase in MEPPs amplitude, which was caused by exogenous CGRP. CONCLUSIONS We propose that the activity of presynaptic CaMKII is necessary for the ryanodine-stimulated release of endogenous CGRP from motor nerve terminals, but CaMKII does not participate in signaling downstream the activation of CGRP-receptors followed by quantal size increase.
Collapse
Affiliation(s)
- Alexander E Gaydukov
- Department of Human and Animal Physiology, Biological Faculty, Lomonosov Moscow State University, Moscow, Russia.,Department of Physiology, Russian National Research Medical University, Moscow, Russia
| | - Olga P Balezina
- Department of Human and Animal Physiology, Biological Faculty, Lomonosov Moscow State University, Moscow, Russia
| |
Collapse
|
15
|
Heinz LP, Kopec W, de Groot BL, Fink RHA. In silico assessment of the conduction mechanism of the Ryanodine Receptor 1 reveals previously unknown exit pathways. Sci Rep 2018; 8:6886. [PMID: 29720700 PMCID: PMC5932038 DOI: 10.1038/s41598-018-25061-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 04/13/2018] [Indexed: 12/18/2022] Open
Abstract
The ryanodine receptor 1 is a large calcium ion channel found in mammalian skeletal muscle. The ion channel gained a lot of attention recently, after multiple independent authors published near-atomic cryo electron microscopy data. Taking advantage of the unprecedented quality of structural data, we performed molecular dynamics simulations on the entire ion channel as well as on a reduced model. We calculated potentials of mean force for Ba2+, Ca2+, Mg2+, K+, Na+ and Cl- ions using umbrella sampling to identify the key residues involved in ion permeation. We found two main binding sites for the cations, whereas the channel is strongly repulsive for chloride ions. Furthermore, the data is consistent with the model that the receptor achieves its ion selectivity by over-affinity for divalent cations in a calcium-block-like fashion. We reproduced the experimental conductance for potassium ions in permeation simulations with applied voltage. The analysis of the permeation paths shows that ions exit the pore via multiple pathways, which we suggest to be related to the experimental observation of different subconducting states.
Collapse
Affiliation(s)
- Leonard P Heinz
- Medical Biophysics Unit, Medical Faculty, Institute of Physiology and Pathophysiology, Heidelberg University, 69120, Heidelberg, Germany.
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany.
| | - Wojciech Kopec
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Bert L de Groot
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Rainer H A Fink
- Medical Biophysics Unit, Medical Faculty, Institute of Physiology and Pathophysiology, Heidelberg University, 69120, Heidelberg, Germany
| |
Collapse
|
16
|
Gartshore CJ, Salib MN, Renshaw AA, Molinski TF. Isolation of bastadin-6-O-sulfate and expedient purifications of bastadins-4, -5 and -6 from extracts of Ianthella basta. Fitoterapia 2018; 126:16-21. [PMID: 29221701 PMCID: PMC6391048 DOI: 10.1016/j.fitote.2017.12.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 11/29/2017] [Accepted: 12/04/2017] [Indexed: 11/17/2022]
Abstract
Bastadin-6-34-O-sulfate ester (8) was isolated from methanol extracts of Ianthella basta. The structure of 8 was characterized by analysis of MS and NMR data, and conversion through acid hydrolysis, to the parent compound, bastadin-6, which was identical by HPLC, MS and NMR with an authentic sample. An improved procedure for procurement of pure samples of bastadins-4 (4), -5 (5) and -6 (6) is described.
Collapse
Affiliation(s)
- Christopher J Gartshore
- Department of Chemistry and Biochemistry, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, 9500 Gilman Drive MC0358, La Jolla, San Diego, CA 92093, United States
| | - Mariam N Salib
- Department of Chemistry and Biochemistry, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, 9500 Gilman Drive MC0358, La Jolla, San Diego, CA 92093, United States
| | - August A Renshaw
- Department of Chemistry and Biochemistry, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, 9500 Gilman Drive MC0358, La Jolla, San Diego, CA 92093, United States
| | - Tadeusz F Molinski
- Department of Chemistry and Biochemistry, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, 9500 Gilman Drive MC0358, La Jolla, San Diego, CA 92093, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, 9500 Gilman Drive MC0358, La Jolla, San Diego, CA 92093, United States.
| |
Collapse
|
17
|
Single-channel recordings of RyR1 at microsecond resolution in CMOS-suspended membranes. Proc Natl Acad Sci U S A 2018; 115:E1789-E1798. [PMID: 29432144 DOI: 10.1073/pnas.1712313115] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Single-channel recordings are widely used to explore functional properties of ion channels. Typically, such recordings are performed at bandwidths of less than 10 kHz because of signal-to-noise considerations, limiting the temporal resolution available for studying fast gating dynamics to greater than 100 µs. Here we present experimental methods that directly integrate suspended lipid bilayers with high-bandwidth, low-noise transimpedance amplifiers based on complementary metal-oxide-semiconductor (CMOS) integrated circuits (IC) technology to achieve bandwidths in excess of 500 kHz and microsecond temporal resolution. We use this CMOS-integrated bilayer system to study the type 1 ryanodine receptor (RyR1), a Ca2+-activated intracellular Ca2+-release channel located on the sarcoplasmic reticulum. We are able to distinguish multiple closed states not evident with lower bandwidth recordings, suggesting the presence of an additional Ca2+ binding site, distinct from the site responsible for activation. An extended beta distribution analysis of our high-bandwidth data can be used to infer closed state flicker events as fast as 35 ns. These events are in the range of single-file ion translocations.
Collapse
|
18
|
Santulli G, Lewis D, des Georges A, Marks AR, Frank J. Ryanodine Receptor Structure and Function in Health and Disease. Subcell Biochem 2018; 87:329-352. [PMID: 29464565 PMCID: PMC5936639 DOI: 10.1007/978-981-10-7757-9_11] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Ryanodine receptors (RyRs) are ubiquitous intracellular calcium (Ca2+) release channels required for the function of many organs including heart and skeletal muscle, synaptic transmission in the brain, pancreatic beta cell function, and vascular tone. In disease, defective function of RyRs due either to stress (hyperadrenergic and/or oxidative overload) or genetic mutations can render the channels leaky to Ca2+ and promote defective disease-causing signals as observed in heat failure, muscular dystrophy, diabetes mellitus, and neurodegerative disease. RyRs are massive structures comprising the largest known ion channel-bearing macromolecular complex and exceeding 3 million Daltons in molecular weight. RyRs mediate the rapid release of Ca2+ from the endoplasmic/sarcoplasmic reticulum (ER/SR) to stimulate cellular functions through Ca2+-dependent processes. Recent advances in single-particle cryogenic electron microscopy (cryo-EM) have enabled the determination of atomic-level structures for RyR for the first time. These structures have illuminated the mechanisms by which these critical ion channels function and interact with regulatory ligands. In the present chapter we discuss the structure, functional elements, gating and activation mechanisms of RyRs in normal and disease states.
Collapse
Affiliation(s)
- Gaetano Santulli
- The Wu Center for Molecular Cardiology, Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, NY, USA
- The Wilf Family Cardiovascular Research Institute and the Einstein-Mount Sinai Diabetes Research Center, Department of Medicine, Albert Einstein College of Medicine - Montefiore University Hospital, New York, NY, USA
| | - Daniel Lewis
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA
| | - Amedee des Georges
- Advanced Science Research Center at the Graduate Center of the City University of New York, New York, NY, USA
- Department of Chemistry & Biochemistry, City College of New York, New York, NY, USA
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY, USA
| | - Andrew R Marks
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA
- Department of Medicine, Columbia University, New York, NY, USA
| | - Joachim Frank
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
- Department of Biological Sciences, Columbia University, New York, NY, USA.
| |
Collapse
|
19
|
Meissner G. The structural basis of ryanodine receptor ion channel function. J Gen Physiol 2017; 149:1065-1089. [PMID: 29122978 PMCID: PMC5715910 DOI: 10.1085/jgp.201711878] [Citation(s) in RCA: 147] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 10/12/2017] [Indexed: 01/25/2023] Open
Abstract
Large-conductance Ca2+ release channels known as ryanodine receptors (RyRs) mediate the release of Ca2+ from an intracellular membrane compartment, the endo/sarcoplasmic reticulum. There are three mammalian RyR isoforms: RyR1 is present in skeletal muscle; RyR2 is in heart muscle; and RyR3 is expressed at low levels in many tissues including brain, smooth muscle, and slow-twitch skeletal muscle. RyRs form large protein complexes comprising four 560-kD RyR subunits, four ∼12-kD FK506-binding proteins, and various accessory proteins including calmodulin, protein kinases, and protein phosphatases. RyRs share ∼70% sequence identity, with the greatest sequence similarity in the C-terminal region that forms the transmembrane, ion-conducting domain comprising ∼500 amino acids. The remaining ∼4,500 amino acids form the large regulatory cytoplasmic "foot" structure. Experimental evidence for Ca2+, ATP, phosphorylation, and redox-sensitive sites in the cytoplasmic structure have been described. Exogenous effectors include the two Ca2+ releasing agents caffeine and ryanodine. Recent work describing the near atomic structures of mammalian skeletal and cardiac muscle RyRs provides a structural basis for the regulation of the RyRs by their multiple effectors.
Collapse
Affiliation(s)
- Gerhard Meissner
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, NC
| |
Collapse
|
20
|
IP 3 receptor signaling and endothelial barrier function. Cell Mol Life Sci 2017; 74:4189-4207. [PMID: 28803370 DOI: 10.1007/s00018-017-2624-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 07/18/2017] [Accepted: 08/08/2017] [Indexed: 12/14/2022]
Abstract
The endothelium, a monolayer of endothelial cells lining vessel walls, maintains tissue-fluid homeostasis by restricting the passage of the plasma proteins and blood cells into the interstitium. The ion Ca2+, a ubiquitous secondary messenger, initiates signal transduction events in endothelial cells that is critical to control of vascular tone and endothelial permeability. The ion Ca2+ is stored inside the intracellular organelles and released into the cytosol in response to environmental cues. The inositol 1,4,5-trisphosphate (IP3) messenger facilitates Ca2+ release through IP3 receptors which are Ca2+-selective intracellular channels located within the membrane of the endoplasmic reticulum. Binding of IP3 to the IP3Rs initiates assembly of IP3R clusters, a key event responsible for amplification of Ca2+ signals in endothelial cells. This review discusses emerging concepts related to architecture and dynamics of IP3R clusters, and their specific role in propagation of Ca2+ signals in endothelial cells.
Collapse
|
21
|
Zalk R, Marks AR. Ca 2+ Release Channels Join the 'Resolution Revolution'. Trends Biochem Sci 2017; 42:543-555. [PMID: 28499500 PMCID: PMC5875148 DOI: 10.1016/j.tibs.2017.04.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 04/02/2017] [Accepted: 04/13/2017] [Indexed: 01/22/2023]
Abstract
Ryanodine receptors (RyRs) are calcium release channels expressed in the sarcoendoplasmic reticula of many cell types including cardiac and skeletal muscle cells. In recent years Ca2+ leak through RyRs has been implicated as a major contributor to the development of diseases including heart failure, muscle myopathies, Alzheimer's disease, and diabetes, making it an important therapeutic target. Recent mammalian RyR1 cryoelectron microscopy (cryo-EM) structures of multiple functional states have clarified longstanding questions including the architecture of the transmembrane (TM) pore and cytoplasmic domains, the location and architecture of the channel gate, ligand-binding sites, and the gating mechanism. As we advance toward complete models of RyRs this new information enables the determination of domain-domain interfaces and the location and structural effects of disease-causing RyR mutations.
Collapse
Affiliation(s)
- Ran Zalk
- The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Andrew R Marks
- Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; Wu Center for Molecular Cardiology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
| |
Collapse
|
22
|
Contacts between the endoplasmic reticulum and other membranes in neurons. Proc Natl Acad Sci U S A 2017; 114:E4859-E4867. [PMID: 28559323 DOI: 10.1073/pnas.1701078114] [Citation(s) in RCA: 307] [Impact Index Per Article: 43.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Close appositions between the membrane of the endoplasmic reticulum (ER) and other intracellular membranes have important functions in cell physiology. These include lipid homeostasis, regulation of Ca2+ dynamics, and control of organelle biogenesis and dynamics. Although these membrane contacts have previously been observed in neurons, their distribution and abundance have not been systematically analyzed. Here, we have used focused ion beam-scanning electron microscopy to generate 3D reconstructions of intracellular organelles and their membrane appositions involving the ER (distance ≤30 nm) in different neuronal compartments. ER-plasma membrane (PM) contacts were particularly abundant in cell bodies, with large, flat ER cisternae apposed to the PM, sometimes with a notably narrow lumen (thin ER). Smaller ER-PM contacts occurred throughout dendrites, axons, and in axon terminals. ER contacts with mitochondria were abundant in all compartments, with the ER often forming a network that embraced mitochondria. Small focal contacts were also observed with tubulovesicular structures, likely to be endosomes, and with sparse multivesicular bodies and lysosomes found in our reconstructions. Our study provides an anatomical reference for interpreting information about interorganelle communication in neurons emerging from functional and biochemical studies.
Collapse
|
23
|
From Stores to Sinks: Structural Mechanisms of Cytosolic Calcium Regulation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 981:215-251. [PMID: 29594864 DOI: 10.1007/978-3-319-55858-5_10] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
All eukaryotic cells have adapted the use of the calcium ion (Ca2+) as a universal signaling element through the evolution of a toolkit of Ca2+ sensor, buffer and effector proteins. Among these toolkit components, integral and peripheral proteins decorate biomembranes and coordinate the movement of Ca2+ between compartments, sense these concentration changes and elicit physiological signals. These changes in compartmentalized Ca2+ levels are not mutually exclusive as signals propagate between compartments. For example, agonist induced surface receptor stimulation can lead to transient increases in cytosolic Ca2+ sourced from endoplasmic reticulum (ER) stores; the decrease in ER luminal Ca2+ can subsequently signal the opening surface channels which permit the movement of Ca2+ from the extracellular space to the cytosol. Remarkably, the minuscule compartments of mitochondria can function as significant cytosolic Ca2+ sinks by taking up Ca2+ in a coordinated manner. In non-excitable cells, inositol 1,4,5 trisphosphate receptors (IP3Rs) on the ER respond to surface receptor stimulation; stromal interaction molecules (STIMs) sense the ER luminal Ca2+ depletion and activate surface Orai1 channels; surface Orai1 channels selectively permit the movement of Ca2+ from the extracellular space to the cytosol; uptake of Ca2+ into the matrix through the mitochondrial Ca2+ uniporter (MCU) further shapes the cytosolic Ca2+ levels. Recent structural elucidations of these key Ca2+ toolkit components have improved our understanding of how they function to orchestrate precise cytosolic Ca2+ levels for specific physiological responses. This chapter reviews the atomic-resolution structures of IP3R, STIM1, Orai1 and MCU elucidated by X-ray crystallography, electron microscopy and NMR and discusses the mechanisms underlying their biological functions in their respective compartments within the cell.
Collapse
|